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        <a href="octant-module.html">Package&nbsp;octant</a> ::
        Module&nbsp;tools
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<h1 class="epydoc">Source Code for <a href="octant.tools-module.html">Module octant.tools</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># encoding: utf-8</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"></tt><tt class="py-docstring">"""Tools for working with ROMS model input and output."""</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"restructuredtext en"</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">warnings</tt> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">numpy</tt> <tt class="py-keyword">as</tt> <tt class="py-name">np</tt> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package octant=octant-module.html"><a title="octant" class="py-name" href="#" onclick="return doclink('link-0', 'octant', 'link-0');">octant</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Module octant.io=octant.io-module.html"><a title="octant.io" class="py-name" href="#" onclick="return doclink('link-1', 'io', 'link-1');">io</a></tt> <tt class="py-keyword">import</tt> <tt id="link-2" class="py-name" targets="Function octant.io.Dataset()=octant.io-module.html#Dataset"><a title="octant.io.Dataset" class="py-name" href="#" onclick="return doclink('link-2', 'Dataset', 'link-2');">Dataset</a></tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">matplotlib</tt> <tt class="py-keyword">import</tt> <tt class="py-name">delaunay</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-3" class="py-name"><a title="octant" class="py-name" href="#" onclick="return doclink('link-3', 'octant', 'link-0');">octant</a></tt><tt class="py-op">.</tt><tt id="link-4" class="py-name" targets="Package octant.extern=octant.extern-module.html"><a title="octant.extern" class="py-name" href="#" onclick="return doclink('link-4', 'extern', 'link-4');">extern</a></tt> <tt class="py-keyword">import</tt> <tt id="link-5" class="py-name" targets="Class octant.extern.greatcircle.GreatCircle=octant.extern.greatcircle.GreatCircle-class.html"><a title="octant.extern.greatcircle.GreatCircle" class="py-name" href="#" onclick="return doclink('link-5', 'GreatCircle', 'link-5');">GreatCircle</a></tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">_iso</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line"> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line"> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line"><tt id="link-6" class="py-name" targets="Variable octant.tools.gc_dist=octant.tools-module.html#gc_dist"><a title="octant.tools.gc_dist" class="py-name" href="#" onclick="return doclink('link-6', 'gc_dist', 'link-6');">gc_dist</a></tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">vectorize</tt><tt class="py-op">(</tt><tt class="py-keyword">lambda</tt> <tt class="py-name">lon1</tt><tt class="py-op">,</tt> <tt class="py-name">lat1</tt><tt class="py-op">,</tt> <tt class="py-name">lon2</tt><tt class="py-op">,</tt> <tt class="py-name">lat2</tt><tt class="py-op">:</tt> \ </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line">                      <tt id="link-7" class="py-name"><a title="octant.extern.greatcircle.GreatCircle" class="py-name" href="#" onclick="return doclink('link-7', 'GreatCircle', 'link-5');">GreatCircle</a></tt><tt class="py-op">(</tt><tt class="py-number">6378137.0</tt><tt class="py-op">,</tt> <tt class="py-number">6356752.3142</tt><tt class="py-op">,</tt> \ </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line">                                  <tt class="py-name">lon1</tt><tt class="py-op">,</tt> <tt class="py-name">lat1</tt><tt class="py-op">,</tt> <tt class="py-name">lon2</tt><tt class="py-op">,</tt> <tt class="py-name">lat2</tt><tt class="py-op">)</tt><tt class="py-op">.</tt><tt class="py-name">distance</tt><tt class="py-op">,</tt> \ </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line">                                  <tt class="py-name">doc</tt><tt class="py-op">=</tt> \ </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line"><tt class="py-string">'''</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line"><tt class="py-string">Usage: dist = roms.gc_dist(lon1, lat1, lon2, lat2)</tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line"><tt class="py-string">       All inputs can be arrays, and obey array broadcasting.</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line"><tt class="py-string">'''</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line"> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line"> </tt>
<a name="rot2d"></a><div id="rot2d-def"><a name="L26"></a><tt class="py-lineno"> 26</tt> <a class="py-toggle" href="#" id="rot2d-toggle" onclick="return toggle('rot2d');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="octant.tools-module.html#rot2d">rot2d</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt> <tt class="py-param">y</tt><tt class="py-op">,</tt> <tt class="py-param">ang</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="rot2d-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="rot2d-expanded"><a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">    <tt class="py-docstring">'''rotate vectors by geometric angle'''</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">    <tt class="py-name">xr</tt> <tt class="py-op">=</tt> <tt id="link-8" class="py-name" targets="Variable octant.grid.BoundaryInteractor.x=octant.grid.BoundaryInteractor-class.html#x,Variable octant.grid.CGrid.x=octant.grid.CGrid-class.html#x"><a title="octant.grid.BoundaryInteractor.x
octant.grid.CGrid.x" class="py-name" href="#" onclick="return doclink('link-8', 'x', 'link-8');">x</a></tt><tt class="py-op">*</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Variable octant.ocean.cos=octant.ocean-module.html#cos,Variable octant.ocean.depths.cos=octant.ocean.depths-module.html#cos,Variable octant.ocean.state.cos=octant.ocean.state-module.html#cos,Variable octant.ocean.step3d_t.cos=octant.ocean.step3d_t-module.html#cos,Variable octant.ocean.time.cos=octant.ocean.time-module.html#cos,Variable octant.ocean.velocity.cos=octant.ocean.velocity-module.html#cos"><a title="octant.ocean.cos
octant.ocean.depths.cos
octant.ocean.state.cos
octant.ocean.step3d_t.cos
octant.ocean.time.cos
octant.ocean.velocity.cos" class="py-name" href="#" onclick="return doclink('link-9', 'cos', 'link-9');">cos</a></tt><tt class="py-op">(</tt><tt class="py-name">ang</tt><tt class="py-op">)</tt> <tt class="py-op">-</tt> <tt id="link-10" class="py-name" targets="Variable octant.grid.BoundaryInteractor.y=octant.grid.BoundaryInteractor-class.html#y,Variable octant.grid.CGrid.y=octant.grid.CGrid-class.html#y"><a title="octant.grid.BoundaryInteractor.y
octant.grid.CGrid.y" class="py-name" href="#" onclick="return doclink('link-10', 'y', 'link-10');">y</a></tt><tt class="py-op">*</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt id="link-11" class="py-name" targets="Variable octant.ocean.depths.sin=octant.ocean.depths-module.html#sin,Variable octant.ocean.sin=octant.ocean-module.html#sin,Variable octant.ocean.state.sin=octant.ocean.state-module.html#sin,Variable octant.ocean.step3d_t.sin=octant.ocean.step3d_t-module.html#sin,Variable octant.ocean.time.sin=octant.ocean.time-module.html#sin,Variable octant.ocean.velocity.sin=octant.ocean.velocity-module.html#sin"><a title="octant.ocean.depths.sin
octant.ocean.sin
octant.ocean.state.sin
octant.ocean.step3d_t.sin
octant.ocean.time.sin
octant.ocean.velocity.sin" class="py-name" href="#" onclick="return doclink('link-11', 'sin', 'link-11');">sin</a></tt><tt class="py-op">(</tt><tt class="py-name">ang</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">    <tt class="py-name">yr</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name"><a title="octant.grid.BoundaryInteractor.x
octant.grid.CGrid.x" class="py-name" href="#" onclick="return doclink('link-12', 'x', 'link-8');">x</a></tt><tt class="py-op">*</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt id="link-13" class="py-name"><a title="octant.ocean.depths.sin
octant.ocean.sin
octant.ocean.state.sin
octant.ocean.step3d_t.sin
octant.ocean.time.sin
octant.ocean.velocity.sin" class="py-name" href="#" onclick="return doclink('link-13', 'sin', 'link-11');">sin</a></tt><tt class="py-op">(</tt><tt class="py-name">ang</tt><tt class="py-op">)</tt> <tt class="py-op">+</tt> <tt id="link-14" class="py-name"><a title="octant.grid.BoundaryInteractor.y
octant.grid.CGrid.y" class="py-name" href="#" onclick="return doclink('link-14', 'y', 'link-10');">y</a></tt><tt class="py-op">*</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt id="link-15" class="py-name"><a title="octant.ocean.cos
octant.ocean.depths.cos
octant.ocean.state.cos
octant.ocean.step3d_t.cos
octant.ocean.time.cos
octant.ocean.velocity.cos" class="py-name" href="#" onclick="return doclink('link-15', 'cos', 'link-9');">cos</a></tt><tt class="py-op">(</tt><tt class="py-name">ang</tt><tt class="py-op">)</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">xr</tt><tt class="py-op">,</tt> <tt class="py-name">yr</tt> </tt>
</div><a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line"> </tt>
<a name="nanmask"></a><div id="nanmask-def"><a name="L33"></a><tt class="py-lineno"> 33</tt> <a class="py-toggle" href="#" id="nanmask-toggle" onclick="return toggle('nanmask');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="octant.tools-module.html#nanmask">nanmask</a><tt class="py-op">(</tt><tt class="py-param">a</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="nanmask-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="nanmask-expanded"><a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">    <tt class="py-docstring">'''Return masked array with mask defined by NaNs.'''</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">masked_where</tt><tt class="py-op">(</tt><tt id="link-16" class="py-name" targets="Variable octant.ocean.depths.isnan=octant.ocean.depths-module.html#isnan,Variable octant.ocean.isnan=octant.ocean-module.html#isnan,Variable octant.ocean.state.isnan=octant.ocean.state-module.html#isnan,Variable octant.ocean.step3d_t.isnan=octant.ocean.step3d_t-module.html#isnan,Variable octant.ocean.time.isnan=octant.ocean.time-module.html#isnan,Variable octant.ocean.velocity.isnan=octant.ocean.velocity-module.html#isnan"><a title="octant.ocean.depths.isnan
octant.ocean.isnan
octant.ocean.state.isnan
octant.ocean.step3d_t.isnan
octant.ocean.time.isnan
octant.ocean.velocity.isnan" class="py-name" href="#" onclick="return doclink('link-16', 'isnan', 'link-16');">isnan</a></tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">a</tt><tt class="py-op">)</tt> </tt>
</div><a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line"> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line"> </tt>
<a name="shrink"></a><div id="shrink-def"><a name="L38"></a><tt class="py-lineno"> 38</tt> <a class="py-toggle" href="#" id="shrink-toggle" onclick="return toggle('shrink');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="octant.tools-module.html#shrink">shrink</a><tt class="py-op">(</tt><tt class="py-param">a</tt><tt class="py-op">,</tt><tt class="py-param">b</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="shrink-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="shrink-expanded"><a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">    <tt class="py-docstring">"""Return array shrunk to fit a specified shape by triming or averaging.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line"><tt class="py-docstring">    a = shrink(array, shape)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line"><tt class="py-docstring">    array is an numpy ndarray, and shape is a tuple (e.g., from</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line"><tt class="py-docstring">    array.shape). a is the input array shrunk such that its maximum</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line"><tt class="py-docstring">    dimensions are given by shape. If shape has more dimensions than</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line"><tt class="py-docstring">    array, the last dimensions of shape are fit.</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt>  <tt class="py-line"><tt class="py-docstring">    as, bs = shrink(a, b)</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt>  <tt class="py-line"><tt class="py-docstring">    If the second argument is also an array, both a and b are shrunk to</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line"><tt class="py-docstring">    the dimensions of each other. The input arrays must have the same</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-docstring">    number of dimensions, and the resulting arrays will have the same</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line"><tt class="py-docstring">    shape.</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line"><tt class="py-docstring">    Example</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line"><tt class="py-docstring">    -------</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; shrink(rand(10, 10), (5, 9, 18)).shape</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt>  <tt class="py-line"><tt class="py-docstring">    (9, 10)</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"><tt class="py-docstring">    &gt;&gt;&gt; map(shape, shrink(rand(10, 10, 10), rand(5, 9, 18)))        </tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt>  <tt class="py-line"><tt class="py-docstring">    [(5, 9, 10), (5, 9, 10)]   </tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line"><tt class="py-docstring">       </tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">     </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">,</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ndarray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">            <tt class="py-keyword">raise</tt> <tt class="py-name">Exception</tt><tt class="py-op">,</tt> \ </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">                  <tt class="py-string">'input arrays must have the same number of dimensions'</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">        <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt id="link-17" class="py-name" targets="Function octant.tools.shrink()=octant.tools-module.html#shrink"><a title="octant.tools.shrink" class="py-name" href="#" onclick="return doclink('link-17', 'shrink', 'link-17');">shrink</a></tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">,</tt><tt class="py-name">b</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">        <tt class="py-name">b</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="octant.tools.shrink" class="py-name" href="#" onclick="return doclink('link-18', 'shrink', 'link-17');">shrink</a></tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">,</tt><tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">,</tt> <tt class="py-name">b</tt><tt class="py-op">)</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">     </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">        <tt class="py-name">b</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-name">b</tt><tt class="py-op">,</tt><tt class="py-op">)</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">     </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt>                <tt class="py-comment"># 1D array is a special case</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">        <tt class="py-name">dim</tt> <tt class="py-op">=</tt> <tt class="py-name">b</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt>                       </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">        <tt class="py-keyword">while</tt> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">dim</tt><tt class="py-op">:</tt>          <tt class="py-comment"># only shrink a</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">dim</tt> <tt class="py-op">-</tt> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;=</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt>  <tt class="py-comment"># trim off edges evenly</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">                <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-name">a</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt>                        <tt class="py-comment"># or average adjacent cells</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">                <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-number">0.5</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">a</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">        <tt class="py-keyword">for</tt> <tt class="py-name">dim_idx</tt> <tt class="py-keyword">in</tt> <tt class="py-name">range</tt><tt class="py-op">(</tt><tt class="py-op">-</tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">            <tt class="py-name">dim</tt> <tt class="py-op">=</tt> <tt class="py-name">b</tt><tt class="py-op">[</tt><tt class="py-name">dim_idx</tt><tt class="py-op">]</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">            <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">swapaxes</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">dim_idx</tt><tt class="py-op">)</tt>        <tt class="py-comment"># put working dim first</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">            <tt class="py-keyword">while</tt> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">&gt;</tt> <tt class="py-name">dim</tt><tt class="py-op">:</tt>          <tt class="py-comment"># only shrink a</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">dim</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;=</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt>  <tt class="py-comment"># trim off edges evenly</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt>  <tt class="py-line">                    <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-name">a</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">-</tt> <tt class="py-name">dim</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt>  <tt class="py-comment"># or average adjacent cells</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line">                    <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-number">0.5</tt><tt class="py-op">*</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">a</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">,</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">            <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">swapaxes</tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">,</tt><tt class="py-name">dim_idx</tt><tt class="py-op">)</tt>        <tt class="py-comment"># swap working dim back</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">     </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">a</tt> </tt>
</div><a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line"> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line"> </tt>
<a name="isoslice"></a><div id="isoslice-def"><a name="L97"></a><tt class="py-lineno"> 97</tt> <a class="py-toggle" href="#" id="isoslice-toggle" onclick="return toggle('isoslice');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="octant.tools-module.html#isoslice">isoslice</a><tt class="py-op">(</tt><tt class="py-param">z</tt><tt class="py-op">,</tt> <tt class="py-param">q</tt><tt class="py-op">,</tt> <tt class="py-param">zo</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">mode</tt><tt class="py-op">=</tt><tt class="py-string">'spline'</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="isoslice-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="isoslice-expanded"><a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">    <tt class="py-docstring">"""Return a slice a 3D field along an isosurface.</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line"><tt class="py-docstring">    result is a a projection of variable at property == isoval in the first</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line"><tt class="py-docstring">    nonsingleton dimension.  In the case when there is more than one zero</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line"><tt class="py-docstring">    crossing, the results are averaged.</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line"><tt class="py-docstring">    EXAMPLE:</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line"><tt class="py-docstring">    Assume two three dimensional variable, s (salt), z (depth), and</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line"><tt class="py-docstring">    u (velicity), all on the same 3D grid.  x and y are the horizontal </tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line"><tt class="py-docstring">    positions, with the same horizontal dimensions as z (the 3D depth </tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line"><tt class="py-docstring">    field).  Here, assume the vertical dimension, that will be projected,</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line"><tt class="py-docstring">    is the first.  </tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line"><tt class="py-docstring">    s_at_m5  = isoslice(s,z,-5);        # s at z == -5</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line"><tt class="py-docstring">    h_at_s30 = isoslice(z,s,30);       # z at s == 30</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line"><tt class="py-docstring">    u_at_s30 = isoslice(u,s,30);       # u at s == 30</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">     </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">mode</tt><tt class="py-op">==</tt><tt class="py-string">'linear'</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">        <tt class="py-name">imode</tt><tt class="py-op">=</tt><tt class="py-number">0</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">    <tt class="py-keyword">elif</tt> <tt class="py-name">mode</tt><tt class="py-op">==</tt><tt class="py-string">'spline'</tt><tt class="py-op">:</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">        <tt class="py-name">imode</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">        <tt class="py-name">imode</tt><tt class="py-op">=</tt><tt class="py-number">1</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">        <tt class="py-keyword">raise</tt> <tt class="py-name">Warning</tt><tt class="py-op">,</tt> <tt class="py-string">'%s not supported, defaulting to splines'</tt> <tt class="py-op">%</tt> <tt class="py-name">mode</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">     </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">    <tt class="py-name">z</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">atleast_3d</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">)</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">    <tt class="py-name">q</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">atleast_3d</tt><tt class="py-op">(</tt><tt class="py-name">q</tt><tt class="py-op">)</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">z</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> <tt class="py-op">==</tt> <tt class="py-name">q</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">,</tt> <tt class="py-string">'z and q must be the same shape'</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">     </tt>
<a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line">    <tt class="py-name">qo</tt> <tt class="py-op">*=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">q</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt>  <tt class="py-line">     </tt>
<a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">    <tt class="py-name">q2d</tt> <tt class="py-op">=</tt> <tt class="py-name">_iso</tt><tt class="py-op">.</tt><tt id="link-19" class="py-name" targets="Function octant.slice.zslice()=octant.slice-module.html#zslice"><a title="octant.slice.zslice" class="py-name" href="#" onclick="return doclink('link-19', 'zslice', 'link-19');">zslice</a></tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">,</tt> <tt class="py-name">q</tt><tt class="py-op">,</tt> <tt class="py-name">zo</tt><tt class="py-op">,</tt> <tt class="py-name">imode</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-name">q2d</tt><tt class="py-op">==</tt><tt class="py-number">1e20</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">        <tt class="py-name">q2d</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">masked_where</tt><tt class="py-op">(</tt><tt class="py-name">q2d</tt><tt class="py-op">==</tt><tt class="py-number">1e20</tt><tt class="py-op">,</tt> <tt class="py-name">q2d</tt><tt class="py-op">)</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">     </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">q2d</tt> </tt>
</div><a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line"> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line"> </tt>
<a name="iso_integrate"></a><div id="iso_integrate-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="iso_integrate-toggle" onclick="return toggle('iso_integrate');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="octant.tools-module.html#iso_integrate">iso_integrate</a><tt class="py-op">(</tt><tt class="py-param">z_w</tt><tt class="py-op">,</tt> <tt class="py-param">q</tt><tt class="py-op">,</tt> <tt class="py-param">z_iso</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="iso_integrate-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="iso_integrate-expanded"><a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">    <tt class="py-name">z_w</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">atleast_3d</tt><tt class="py-op">(</tt><tt class="py-name">z_w</tt><tt class="py-op">)</tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">    <tt class="py-name">q</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">atleast_3d</tt><tt class="py-op">(</tt><tt class="py-name">q</tt><tt class="py-op">)</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">z_iso</tt><tt class="py-op">,</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">MaskedArray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">        <tt class="py-name">z_iso</tt> <tt class="py-op">=</tt> <tt class="py-name">z_iso</tt><tt class="py-op">.</tt><tt class="py-name">filled</tt><tt class="py-op">(</tt><tt class="py-number">1e20</tt><tt class="py-op">)</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">    <tt class="py-name">z_iso</tt> <tt class="py-op">*=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">q</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">_iso</tt><tt class="py-op">.</tt><tt class="py-name">integrate</tt><tt class="py-op">(</tt><tt class="py-name">z_w</tt><tt class="py-op">,</tt> <tt class="py-name">q</tt><tt class="py-op">,</tt> <tt class="py-name">z_iso</tt><tt class="py-op">)</tt> </tt>
</div><a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line"> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line"> </tt>
<a name="surface"></a><div id="surface-def"><a name="L146"></a><tt class="py-lineno">146</tt> <a class="py-toggle" href="#" id="surface-toggle" onclick="return toggle('surface');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="octant.tools-module.html#surface">surface</a><tt class="py-op">(</tt><tt class="py-param">z</tt><tt class="py-op">,</tt> <tt class="py-param">q</tt><tt class="py-op">,</tt> <tt class="py-param">qo</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="surface-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="surface-expanded"><a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-string">'z must be 3D'</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">q</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">3</tt><tt class="py-op">,</tt> <tt class="py-string">'q must be 3D'</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">z</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> <tt class="py-op">==</tt> <tt class="py-name">q</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">,</tt> <tt class="py-string">'z and q must be the same size'</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">    <tt class="py-name">qo</tt> <tt class="py-op">=</tt> <tt class="py-name">qo</tt> <tt class="py-op">*</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ones</tt><tt class="py-op">(</tt><tt class="py-name">q</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">    <tt class="py-name">z_iso</tt> <tt class="py-op">=</tt> <tt class="py-name">_iso</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Function octant.slice.surface()=octant.slice-module.html#surface,Function octant.tools.surface()=octant.tools-module.html#surface"><a title="octant.slice.surface
octant.tools.surface" class="py-name" href="#" onclick="return doclink('link-20', 'surface', 'link-20');">surface</a></tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">,</tt> <tt class="py-name">q</tt><tt class="py-op">,</tt> <tt class="py-name">qo</tt><tt class="py-op">)</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">any</tt><tt class="py-op">(</tt><tt class="py-name">z_iso</tt><tt class="py-op">==</tt><tt class="py-number">1e20</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">masked_where</tt><tt class="py-op">(</tt><tt class="py-name">z_iso</tt><tt class="py-op">==</tt><tt class="py-number">1e20</tt><tt class="py-op">,</tt> <tt class="py-name">z_iso</tt><tt class="py-op">)</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">z_iso</tt> </tt>
</div><a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line"> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line"> </tt>
<a name="N2"></a><div id="N2-def"><a name="L158"></a><tt class="py-lineno">158</tt> <a class="py-toggle" href="#" id="N2-toggle" onclick="return toggle('N2');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="octant.tools-module.html#N2">N2</a><tt class="py-op">(</tt><tt class="py-param">rho</tt><tt class="py-op">,</tt> <tt class="py-param">z</tt><tt class="py-op">,</tt> <tt class="py-param">rho_0</tt><tt class="py-op">=</tt><tt class="py-number">1000.0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="N2-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="N2-expanded"><a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">    <tt class="py-docstring">'''Return the stratification frequency</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line"><tt class="py-docstring">    Parameters</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line"><tt class="py-docstring">    ----------</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line"><tt class="py-docstring">    rho : array_like</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line"><tt class="py-docstring">        density [kg/m^3]</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line"><tt class="py-docstring">    z : array_like</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line"><tt class="py-docstring">        depths [m] (positive upward)</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line"><tt class="py-docstring">    Returns</tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"><tt class="py-docstring">    -------</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt>  <tt class="py-line"><tt class="py-docstring">    N2 : array_like</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line"><tt class="py-docstring">        Stratification frequency [1/s], where the vertical dimension (the</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line"><tt class="py-docstring">        first dimension) is one less than the input arrays.</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line"><tt class="py-docstring">    '''</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">    <tt class="py-name">rho</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">rho</tt><tt class="py-op">)</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">    <tt class="py-name">z</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">)</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">rho</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt> <tt class="py-op">==</tt> <tt class="py-name">z</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">,</tt> <tt class="py-string">'rho and z must have the same shape.'</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">    <tt class="py-name">r_z</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">diff</tt><tt class="py-op">(</tt><tt class="py-name">rho</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> <tt class="py-op">/</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">diff</tt><tt class="py-op">(</tt><tt class="py-name">z</tt><tt class="py-op">,</tt> <tt class="py-name">axis</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-op">-</tt><tt class="py-op">(</tt><tt class="py-number">9.8</tt> <tt class="py-op">/</tt> <tt class="py-name">rho_0</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">r_z</tt> </tt>
</div><a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line"> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line"> </tt>
<a name="arg_nearest"></a><div id="arg_nearest-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="arg_nearest-toggle" onclick="return toggle('arg_nearest');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="octant.tools-module.html#arg_nearest">arg_nearest</a><tt class="py-op">(</tt><tt class="py-param">x</tt><tt class="py-op">,</tt> <tt class="py-param">xo</tt><tt class="py-op">,</tt> <tt class="py-param">scale</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="arg_nearest-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="arg_nearest-expanded"><a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">    <tt class="py-docstring">"""returns indices of closest point in an N arrays.</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line"><tt class="py-docstring">    Parameters</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line"><tt class="py-docstring">    ----------</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line"><tt class="py-docstring">    x : tuple of N ndarray objects</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line"><tt class="py-docstring">        N ndarrays of coordinate variables that define an N-dimensional space.</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line"><tt class="py-docstring">        All arrays must have the same shape.</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line"><tt class="py-docstring">    xo : array_like</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line"><tt class="py-docstring">        len(N) array representing the query point.</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line"><tt class="py-docstring">    scale : array_like, optional</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line"><tt class="py-docstring">        len(N) array of values to multiply by each coordinate variable by</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line"><tt class="py-docstring">        before distance is calculated.</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line"><tt class="py-docstring">    Returns</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line"><tt class="py-docstring">    -------</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line"><tt class="py-docstring">    indexes : ndarray</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line"><tt class="py-docstring">        An array of indicies such that (x[idx], y[idx], z[idx], ...) is the</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line"><tt class="py-docstring">        closest point to xo</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line"><tt class="py-docstring">    </tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">     </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">    <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-21" class="py-name"><a title="octant.grid.BoundaryInteractor.x
octant.grid.CGrid.x" class="py-name" href="#" onclick="return doclink('link-21', 'x', 'link-8');">x</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xo</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> \ </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">        <tt class="py-string">'must have %d %d-dimensional arrays'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xo</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xo</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">     </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">dim</tt><tt class="py-op">,</tt> <tt class="py-name">p</tt> <tt class="py-keyword">in</tt> <tt class="py-name">enumerate</tt><tt class="py-op">(</tt><tt id="link-22" class="py-name"><a title="octant.grid.BoundaryInteractor.x
octant.grid.CGrid.x" class="py-name" href="#" onclick="return doclink('link-22', 'x', 'link-8');">x</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xo</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> \ </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">            <tt class="py-string">'dimensions of array %d must be %d'</tt> <tt class="py-op">%</tt> <tt class="py-op">(</tt><tt class="py-name">dim</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">xo</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">     </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt class="py-name">scale</tt><tt class="py-op">:</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">        <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-23" class="py-name"><a title="octant.grid.BoundaryInteractor.x
octant.grid.CGrid.x" class="py-name" href="#" onclick="return doclink('link-23', 'x', 'link-8');">x</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">scale</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> \ </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">            <tt class="py-string">'dimensions of array and scale must be identical'</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">        <tt id="link-24" class="py-name"><a title="octant.grid.BoundaryInteractor.x
octant.grid.CGrid.x" class="py-name" href="#" onclick="return doclink('link-24', 'x', 'link-8');">x</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">*</tt><tt class="py-name">q</tt> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">,</tt> <tt class="py-name">q</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt id="link-25" class="py-name"><a title="octant.grid.BoundaryInteractor.x
octant.grid.CGrid.x" class="py-name" href="#" onclick="return doclink('link-25', 'x', 'link-8');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">scale</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">        <tt class="py-name">xo</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">p</tt><tt class="py-op">*</tt><tt class="py-name">q</tt> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt class="py-name">p</tt><tt class="py-op">,</tt> <tt class="py-name">q</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-name">xo</tt><tt class="py-op">,</tt> <tt class="py-name">scale</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">     </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">    <tt class="py-name">q</tt> <tt class="py-op">=</tt> <tt class="py-name">reduce</tt><tt class="py-op">(</tt><tt class="py-name">np</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Variable octant.ocean.add=octant.ocean-module.html#add,Variable octant.ocean.depths.add=octant.ocean.depths-module.html#add,Variable octant.ocean.state.add=octant.ocean.state-module.html#add,Variable octant.ocean.step3d_t.add=octant.ocean.step3d_t-module.html#add,Variable octant.ocean.time.add=octant.ocean.time-module.html#add,Variable octant.ocean.velocity.add=octant.ocean.velocity-module.html#add"><a title="octant.ocean.add
octant.ocean.depths.add
octant.ocean.state.add
octant.ocean.step3d_t.add
octant.ocean.time.add
octant.ocean.velocity.add" class="py-name" href="#" onclick="return doclink('link-26', 'add', 'link-26');">add</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="octant.grid.BoundaryInteractor.y
octant.grid.CGrid.y" class="py-name" href="#" onclick="return doclink('link-27', 'y', 'link-10');">y</a></tt><tt class="py-op">-</tt><tt class="py-name">yo</tt><tt class="py-op">)</tt><tt class="py-op">**</tt><tt class="py-number">2</tt> <tt class="py-keyword">for</tt> <tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="octant.grid.BoundaryInteractor.y
octant.grid.CGrid.y" class="py-name" href="#" onclick="return doclink('link-28', 'y', 'link-10');">y</a></tt><tt class="py-op">,</tt> <tt class="py-name">yo</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="octant.grid.BoundaryInteractor.x
octant.grid.CGrid.x" class="py-name" href="#" onclick="return doclink('link-29', 'x', 'link-8');">x</a></tt><tt class="py-op">,</tt> <tt class="py-name">xo</tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">where</tt><tt class="py-op">(</tt><tt class="py-name">q</tt> <tt class="py-op">==</tt> <tt class="py-name">q</tt><tt class="py-op">.</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line"> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line"> </tt>
<a name="extrapolate_mask"></a><div id="extrapolate_mask-def"><a name="L221"></a><tt class="py-lineno">221</tt> <a class="py-toggle" href="#" id="extrapolate_mask-toggle" onclick="return toggle('extrapolate_mask');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="octant.tools-module.html#extrapolate_mask">extrapolate_mask</a><tt class="py-op">(</tt><tt class="py-param">a</tt><tt class="py-op">,</tt> <tt class="py-param">mask</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="extrapolate_mask-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="extrapolate_mask-expanded"><a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-30" class="py-name" targets="Variable octant.grid.CGrid.mask=octant.grid.CGrid-class.html#mask"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-30', 'mask', 'link-30');">mask</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">and</tt> <tt class="py-keyword">not</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">,</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">MaskedArray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>  </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">a</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">    <tt class="py-keyword">if</tt> <tt id="link-31" class="py-name"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-31', 'mask', 'link-30');">mask</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line">        <tt id="link-32" class="py-name"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-32', 'mask', 'link-30');">mask</a></tt> <tt class="py-op">=</tt> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-33', 'mask', 'link-30');">mask</a></tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt>  <tt class="py-line">    <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">,</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">ma</tt><tt class="py-op">.</tt><tt class="py-name">MaskedArray</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt>  <tt class="py-line">            <tt id="link-34" class="py-name"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-34', 'mask', 'link-30');">mask</a></tt> <tt class="py-op">=</tt> <tt id="link-35" class="py-name"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-35', 'mask', 'link-30');">mask</a></tt> <tt class="py-op">|</tt> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-36" class="py-name"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-36', 'mask', 'link-30');">mask</a></tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt>  <tt class="py-line">    <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-name">a</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt>    <tt class="py-comment"># make a copy of array a</tt> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt>  <tt class="py-line">    <tt class="py-name">jj</tt><tt class="py-op">,</tt> <tt class="py-name">ii</tt> <tt class="py-op">=</tt> <tt class="py-name">indices</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">.</tt><tt class="py-name">shape</tt><tt class="py-op">)</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt>  <tt class="py-line">    <tt class="py-name">igood</tt> <tt class="py-op">=</tt> <tt class="py-name">ii</tt><tt class="py-op">[</tt><tt class="py-op">~</tt><tt id="link-37" class="py-name"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-37', 'mask', 'link-30');">mask</a></tt><tt class="py-op">]</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt>  <tt class="py-line">    <tt class="py-name">jgood</tt> <tt class="py-op">=</tt> <tt class="py-name">jj</tt><tt class="py-op">[</tt><tt class="py-op">~</tt><tt id="link-38" class="py-name"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-38', 'mask', 'link-30');">mask</a></tt><tt class="py-op">]</tt> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt>  <tt class="py-line">    <tt class="py-name">ibad</tt> <tt class="py-op">=</tt> <tt class="py-name">ii</tt><tt class="py-op">[</tt><tt id="link-39" class="py-name"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-39', 'mask', 'link-30');">mask</a></tt><tt class="py-op">]</tt> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt>  <tt class="py-line">    <tt class="py-name">jbad</tt> <tt class="py-op">=</tt> <tt class="py-name">jj</tt><tt class="py-op">[</tt><tt id="link-40" class="py-name"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-40', 'mask', 'link-30');">mask</a></tt><tt class="py-op">]</tt> </tt>
<a name="L235"></a><tt class="py-lineno">235</tt>  <tt class="py-line">    <tt class="py-name">tri</tt> <tt class="py-op">=</tt> <tt class="py-name">delaunay</tt><tt class="py-op">.</tt><tt class="py-name">Triangulation</tt><tt class="py-op">(</tt><tt class="py-name">igood</tt><tt class="py-op">,</tt> <tt class="py-name">jgood</tt><tt class="py-op">)</tt> </tt>
<a name="L236"></a><tt class="py-lineno">236</tt>  <tt class="py-line">    <tt class="py-comment"># interpolate from the good points (mask == 1)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">interp</tt> <tt class="py-op">=</tt> <tt class="py-name">tri</tt><tt class="py-op">.</tt><tt class="py-name">nn_extrapolator</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">[</tt><tt class="py-op">~</tt><tt id="link-41" class="py-name"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-41', 'mask', 'link-30');">mask</a></tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt>  <tt class="py-line">    <tt class="py-comment"># to the bad points (mask == 0)</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt>  <tt class="py-line"><tt class="py-comment"></tt>    <tt class="py-name">a</tt><tt class="py-op">[</tt><tt id="link-42" class="py-name"><a title="octant.grid.CGrid.mask" class="py-name" href="#" onclick="return doclink('link-42', 'mask', 'link-30');">mask</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">interp</tt><tt class="py-op">(</tt><tt class="py-name">ibad</tt><tt class="py-op">,</tt> <tt class="py-name">jbad</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">a</tt> </tt>
</div><a name="L241"></a><tt class="py-lineno">241</tt>  <tt class="py-line"> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt>  <tt class="py-line"> </tt>
<a name="Transect_extrapolator"></a><div id="Transect_extrapolator-def"><a name="L243"></a><tt class="py-lineno">243</tt> <a class="py-toggle" href="#" id="Transect_extrapolator-toggle" onclick="return toggle('Transect_extrapolator');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="octant.tools.Transect_extrapolator-class.html">Transect_extrapolator</a><tt class="py-op">(</tt><tt class="py-base-class">object</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Transect_extrapolator-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Transect_extrapolator-expanded"><a name="L244"></a><tt class="py-lineno">244</tt>  <tt class="py-line">    <tt class="py-docstring">"""</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt>  <tt class="py-line"><tt class="py-docstring">    General Transect object</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="Transect_extrapolator.__init__"></a><div id="Transect_extrapolator.__init__-def"><a name="L247"></a><tt class="py-lineno">247</tt> <a class="py-toggle" href="#" id="Transect_extrapolator.__init__-toggle" onclick="return toggle('Transect_extrapolator.__init__');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="octant.tools.Transect_extrapolator-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">xg</tt><tt class="py-op">,</tt> <tt class="py-param">yg</tt><tt class="py-op">,</tt> <tt class="py-param">verts</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Transect_extrapolator.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Transect_extrapolator.__init__-expanded"><a name="L248"></a><tt class="py-lineno">248</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xg</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">xg</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yg</tt> <tt class="py-op">=</tt> <tt class="py-name">np</tt><tt class="py-op">.</tt><tt class="py-name">asarray</tt><tt class="py-op">(</tt><tt class="py-name">yg</tt><tt class="py-op">)</tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-43" class="py-name" targets="Variable octant.grid.BoundaryInteractor.verts=octant.grid.BoundaryInteractor-class.html#verts"><a title="octant.grid.BoundaryInteractor.verts" class="py-name" href="#" onclick="return doclink('link-43', 'verts', 'link-43');">verts</a></tt> <tt class="py-op">=</tt> <tt id="link-44" class="py-name"><a title="octant.grid.BoundaryInteractor.verts" class="py-name" href="#" onclick="return doclink('link-44', 'verts', 'link-43');">verts</a></tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_xv</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_yv</tt> <tt class="py-op">=</tt> <tt class="py-name">zip</tt><tt class="py-op">(</tt><tt class="py-op">*</tt><tt id="link-45" class="py-name"><a title="octant.grid.BoundaryInteractor.verts" class="py-name" href="#" onclick="return doclink('link-45', 'verts', 'link-43');">verts</a></tt><tt class="py-op">)</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt>  <tt class="py-line">         </tt>
<a name="L253"></a><tt class="py-lineno">253</tt>  <tt class="py-line">        <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_tri</tt> <tt class="py-op">=</tt> <tt class="py-name">delaunay</tt><tt class="py-op">.</tt><tt class="py-name">Triangulation</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">xg</tt><tt class="py-op">.</tt><tt class="py-name">flat</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">yg</tt><tt class="py-op">.</tt><tt class="py-name">flat</tt><tt class="py-op">)</tt> </tt>
</div><a name="L254"></a><tt class="py-lineno">254</tt>  <tt class="py-line">     </tt>
<a name="Transect_extrapolator.extrapolate"></a><div id="Transect_extrapolator.extrapolate-def"><a name="L255"></a><tt class="py-lineno">255</tt> <a class="py-toggle" href="#" id="Transect_extrapolator.extrapolate-toggle" onclick="return toggle('Transect_extrapolator.extrapolate');">-</a><tt class="py-line">    <tt class="py-keyword">def</tt> <a class="py-def-name" href="octant.tools.Transect_extrapolator-class.html#extrapolate">extrapolate</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">prop</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Transect_extrapolator.extrapolate-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Transect_extrapolator.extrapolate-expanded"><a name="L256"></a><tt class="py-lineno">256</tt>  <tt class="py-line">        <tt class="py-docstring">"""</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt>  <tt class="py-line"><tt class="py-docstring">        extrapolate transect values in the prop datafield</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt>  <tt class="py-line"><tt class="py-docstring">        """</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt>  <tt class="py-line">        <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_tri</tt><tt class="py-op">.</tt><tt class="py-name">nn_interpolator</tt><tt class="py-op">(</tt><tt class="py-name">prop</tt><tt class="py-op">)</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_xv</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">_yv</tt><tt class="py-op">)</tt> </tt>
</div></div><a name="L260"></a><tt class="py-lineno">260</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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